Because placing tiles that have any sort of transparency doesn’t look well (it changes tile’s bg color to black. Adding second layer to ground tiles, so e.g. tile with transparency could be placed on dirt would fix it.
There are quite few transparent tiles which are unusable because of this issue.
Generally tiles in tile mode aren’t meant to be transparent. Unless I misunderstand you and you mean the ground layer in the object mode. Tiles in tile mode aren’t meant to be used as structures. They give textures to the ground, and having a transparent ground could be made in a different way. I’m not sure what you would like to do with transparent tiles on the ground. But some structures in tile mode do give a black background since it doesn’t fill up the whole 32×32 pixels. And tiles in tile mode should fill up all the 32×32. I’m not sure why there are tiles in there that don’t fill up all of the space.